Yep, common problem - called the Z order problem. The items are still there, just hiding behind other items. I recommend using the Tags Pane rather than the Order Pane to adjust reading order. Use the Content Pane to readjust the order in the visual representation of the document. For example, if text goes into hiding behind a shaded box, in the Content Pane move the shaded box to a position before the text. Text will reappear. I posted a video on this topic that you might find helpful - z order problem - YouTube
Fantastic. I watched the video and have one question: Why does an item that is supposed to be behind another item have to be placed before it in the content panel?
I mean, I get that it's just how Acrobat works, but I wondered if you knew the logic behind it.
Sorry, don't know. I guess it had to be one way or the other. Maybe John Warnock flipped a coin?